Seattle supercomputing company Cray (NASDAQ: CRAY) is cutting about 50 jobs as it reconfigures its employee mix, according to a regulatory filing. The company didn’t specify what types of jobs were being cut, or say where they were located, other than to indicate the losses aren’t concentrated in any particular place or category.

Cray’s headquarters are in Seattle and its two other major domestic facilities are in St. Paul, MN, and Chippewa Falls, WI. Cray said the layoffs would be “substantially offset” by future additions in key areas including software development and custom engineering. Cray said those hiring plans mean its overall headcount will stay roughly flat this year. It looks like the news was first reported locally by The Seattle Times’ Brier Dudley.

Spokesman Nick Davis says Cray had about 885 employees total at the end of 2010. The company’s job-posting site shows four jobs currently open in Seattle: director of compensation and benefits, financial analyst, senior product marketing manager and a software developer.

“We need to hire a significant number of employees in critical areas of the company to deliver on our growth plan, and we couldn’t do the hiring we need on top of our current cost structure,” Davis says. “This is a very difficult decision for us. We are working very hard to provide the support for those people who are directly impacted.”

Cray, a historic giant of the computing business, was on our radar screen quite a few times in 2010 as it continued to rack up large contracts worldwide. That included about $60 million from the University of Stuttgart, a $25 million partnership with Nvidia for DARPA projects, and $47 million from the Department of Energy.

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SAIC’s plans to move its corporate headquarters from San Diego, where the company was founded in 1969, to McLean, VA, may rank as one of the defense contractor’s worst-kept secrets. Today the company also known as Science Applications International Corp. made it official. In a statement issued by the company, new CEO Walt Havenstein says, “This move will formally relocate the corporate executive leadership team closer to our federal government customers enabling us to better respond quickly and efficiently to their critical needs, while maintaining a significant presence in San Diego.”

SAIC spokeswoman Laura Luke tells me by email that the relocation only affects corporate functions, and that roughly 20 corporate positions are being considered for relocation to McLean. These moves would take place by next summer, and operational units directly supporting customers in San Diego will not be affected, Luke says.

Virginia Gov. Tim Kaine hailed the move, calling SAIC a “technology and defense powerhouse” and disclosing that the company plans to invest $25 million and add 1,200 new jobs in the Northern Virginia area over the next three years. About 17,500 of SAIC’s estimated 45,000-employee workforce already works in the metropolitan Washington, D.C., area.

SAIC ranks among a handful of Fortune 500 companies in San Diego. The company had annual revenues of $10.1 billion for its fiscal year that ended Jan. 31.

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[Updated 9/18/09 2:45 pm PT. See below.] SAIC, the secretive defense contractor that was founded in San Diego 40 years ago by nuclear physicist J. Robert Beyster, apparently plans to announce the relocation of its corporate headquarters to Tysons Corner, VA, sometime next week.

The looming announcement from Virginia Gov. Timothy M. Kaine was first reported by The Washington Post on its Virginia Politics blog, which cited unnamed “government and business leaders.” The SAIC employee who called it to my attention says “anybody affiliated with corporate [operations] in San Diego is hearing that giant sucking sound.” San Diego’s loss is Virginia’s gain. The Post’s Amy Gardner says the move is expected to bring more than 1,000 “high-paying jobs” to Northern Virginia.

For a company as large as SAIC, relocating the corporate headquarters would likely affect close to 1,000 San Diego employees working in finance, accounting, legal, and other high-level corporate and administrative functions. [Updates with comment from SAIC.] A spokeswoman for SAIC, also known as Science Applications International Corp., responded to my query by email, saying only, “SAIC has not made an announcement about its headquarters.”

The move appears most likely to be announced Monday, when Walt Havenstein takes over as SAIC’s new CEO. Halvenstein, the former head of North American operations for BAE Systems, was named in June to succeed Ken Dahlberg as CEO at the company. Dahlberg, a former General Dynamics executive who succeeded Beyster as CEO in 2003, plans to remain chairman of SAIC’s board of directors.

Dahlberg began shifting many of the company’s high-level functions to Virginia in 2006, when SAIC had about 5,000 employees in San Diego and more than 16,000 at its campus near McLean, VA.

The bulk of SAIC’s workforce has resided in Virginia for decades, because of the company’s focus on providing specialized research and engineering work under contracts for defense and intelligence agencies, as well as energy, health, environment, and other areas. (Because of SAIC’s deep expertise in IT integration and systems support, I think of the company as the systems administrator for the CIA and other intelligence agencies.)

Beyster founded SAIC with a small group of scientists in 1969 to provide contract research services for the government on nuclear weapons and in other fields. The company now has about 45,000 employees in 150 cities worldwide.

SAIC's Virginia Campus

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In the 11 years since Andrew Hibbs started QUASAR, the privately held company has flourished by developing a smorgasbord of sophisticated sensing technologies under various government research and development contracts.

I met Hibbs more than a decade ago, during the formative years of San Diego’s Quantum Magnetics, where he led development of advanced electromagnetic sensors so sensitive they could detect the unique molecular resonance of explosives. His work resulted in the first commercially available explosives detector using Nuclear Quadrapole Resonance, a technology akin to magnetic resonance imaging (MRI) scans that are commonly used in medical diagnostics.

Hibbs founded QUASAR in 1998, after InVision Technologies acquired Quantum Magnetics (and General Electric acquired InVision in 2004). Hibbs acquired a penchant for studying the quantum phenomena at the core of such technologies while earning his PhD in physics at England’s Cambridge University. In fact, he named the company for Quantum Applied Science & Research.

Since QUASAR was founded, Hibbs has formed a group of several related companies focused on biomedical, geophysical, and various military applications of electromagnetic sensing. The company bills itself as a world leader in low-frequency electromagnetic sensing systems that operate at room temperatures (at frequencies from 0.01 Hz to 5 MHz).

When I dropped in for a briefing earlier this week, Hibbs was out of town, so I met with Lowell Burnett, chief technology officer for QUASAR Federal Systems and at least four other PhDs who oversee different development efforts within the group. Burnett told me the QUASAR group has grown to about 70 employees (at least a third are former Quantum Magnetics employees), funded solely by revenues from government contracts.

Burnett says QUASAR’s scientists have made steady advances in electromagnetic sensors, particularly in electric field sensors, with each group applying … Next Page »

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SAIC’s acquisition of an Oklahoma engineering company in 2007 could yield a substantial new revenue source for the San Diego-based government contractor. The company also known as Science Applications International Corp. (NYSE: SAI) said earlier this week its Benham Companies subsidiary was recently awarded an Energy Savings Performance Contract by the U.S. Department of Energy.

The DOE contract qualifies Benham for work to be awarded under a 2007 law that requires federal agencies to reduce their energy “intensity” by 30 percent from 2003 levels and water consumption by 16 percent from 2007 usage levels. SAIC did not disclose financial terms when it acquired Benham in mid-2007.

The federal government is the largest single user of energy in the United States. The DOE award enables the Oklahoma City-based firm to get project orders that could total as much as $5 billion over seven years if all options are exercised. Benham designs and builds industrial facilities, including oil refineries and public buildings, and specializes in designing and installing energy management technologies.

SAIC says its Benham subsidiary also won a second Energy Savings Performance Contract from the U.S. Army Corps of Engineers, although the total contract ceiling for that work is only $50 million over six years if all options are exercised.

Under the Energy Savings Performance contract, SAIC spokeswoman Melissa Koskovich says Benham is basically pre-qualified to bid for energy-saving projects, but a big difference is the company must arrange its own financing. Once a federal agency issues a contract to Benham for a particular project, Benham must obtain the necessary financing, and design and build the project. The government agency pays the company for its work over a specified period from the savings it gains from the reduced costs of its energy or water utility bills.

The DOE says the contractor must guarantee that its energy or water improvements will generate savings for the agency. After the contract ends, any continuing cost savings accrue to the agency.

SAIC’s Benham subsidiary was among 16 companies to get identical Energy Savings and Performance Contracts in December under the DOE’s Federal Energy Management Program. All 16 companies are listed here

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Which San Diego firms are the most inventive? When the 2008 year-end patent figures recently became available, we decided to find out. Xconomy is listing the top 25 patent winners in the San Diego region below, based on data provided by IFI Patent Intelligence of Wilmington, DE. Our compilation includes a few surprises.

San Diego-based Qualcomm might reasonably be expected to lead the region in patents issued in 2008—and with its longtime leadership in wireless technology, indeed that was the case. Yet the company that garnered the second-highest number of patents last year is not a major engineering research and development conglomerate like SAIC, but Callaway Golf, the Carlsbad-based maker of high-end golf clubs.

Some also might find it surprising to see a startup company in the top 10, since prosecuting patents is neither cheap nor routine—and startups are typically founded on a sole technology. Yet San Diego’s Fallbrook Technologies ranks No. 8 on our list, with 21 patents issued in 2008, which was a decline from 31 patents awarded to Fallbrook in 2007. The venture-backed startup has more than 300 patents issued or pending for its revolutionary transmission design.

In preparing the data, IFI analyzed 2008 utility patents assigned to companies by the U.S. Patent and Trademark Office. IBM continued to top the national list in 2008, with 4,186 patents issued, and U.S. companies accounted for 49 percent of all … Next Page »

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